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ONLINE SUPPLEMENTARY MATERIAL
Supplementary Table 1: Cluster 1 Transcripts.
Probe
Set ID
1377192_a_at
1373718_at
1370381_at
1387470_at
1372755_at
1390107_at
1390117_at
1375215_x_at
1367850_at
1374570_at
1376427_a_at
1390042_at
1389377_at
1370510_a_at
1398362_at
1398950_at
1377375_at
1386918_a_at
1376788_at
1390672_at
1373515_at
1399005_at
1367867_at
1373542_at
1390381_at
1373312_at
1375856_at
1372536_at
1398902_at
1375933_at
1389408_at
1374753_at
1368227_at
1367838_at
1372004_at
1368336_at
1398891_at
1388484_at
1375216_at
1388408_at
1387361_s_at
1368184_at
1374747_at
1388318_at
Accession #
BM384629
BM384071
U61729
NM_031699
AI102073
BG670294
BG372455
BE109558
NM_053843
AI012474
AI029729
AI071166
AA851803
AB012600
AI011448
BI275914
AA944898
AF087827
AA818353
BG381258
BI275737
BG673380
NM_013222
BM386306
BG379358
BI295064
AI102258
AI105042
BF282978
BM392116
BG379338
AI105113
NM_031664
NM_017074
AI102065
NM_017126
AI103129
BI296084
AA850909
AA800199
NM_053291
NM_130430
BM384279
BI279760
Correlation
0.989
0.98
0.97
0.967
0.962
0.959
0.954
0.951
0.951
0.95
0.95
0.944
0.943
0.937
0.936
0.935
0.931
0.931
0.928
0.927
0.92
0.919
0.919
0.914
0.912
0.91
0.904
0.902
0.9
0.897
0.893
0.892
0.891
0.882
0.881
0.877
0.869
0.86
0.839
0.836
0.825
0.808
0.804
0.802
Abbreviation
Gene Name
Gene Function
Clpx
caseinolytic peptidase X
tubulin, beta 2
proline-rich nuclear receptor coactivator 1, F-box protein 11
norvegicus claudin 1
T-cell differentiation protein 2, MAL proteolipid protein 2
synaptotagmin-like 2
yippee-like 2 (Drosophila)
pyroglutamyl-peptidase I
Fc receptor, IgG, low affinity III
1-acylglycerol-3-phosphate O-acyltransferase 2
glycine decarboxylase
EST
insulin induced gene 2
aryl hydrocarbon receptor nuclear translocator-like
Notch homolog 2 (Drosophila)
sciellin
aminoadipate-semialdehyde synthase
opioid receptor, sigma 1
death associated protein kinase 1
reprimo
galectin-5 (RL-18)
protein phosphatase 2, regulatory subunit B
augmenter of liver regeneration; growth factor, erv1-like
sphingosine kinase 2 (Sphk2)
xeroderma pigmentosum, complementation group C
paroxysmal nonkinesiogenic dyskinesia
4-aminobutyrate aminotransferase
chaperone, ABC1 activity of bc1 complex like
mKIAA0664 protein
claudin 2
ribonucleotide reductase M2
PAP associated domain containing 4
solute carrier family 28, a2
CTL target antigen (Cth)
heme binding protein 1
ferredoxin 1.
mitochondrial ribosomal protein L15
ubiquitin-conjugating enzyme E2C
poliovirus receptor-related 2
proline rich 13
phosphoglycerate kinase 1
proteasome (prosome, macropain) 26S subunit, non-ATPase, 9
PFTAIRE protein kinase 1
phosphoglycerate kinase 1
protein chaperone to mitochondria
microtubules, cytoskeleton
type II protein arginine methyltransferase (nuclear)
Ca(2+)-independent cell adhesion activity
basolateral-to-apical transcytosis
vesicle trafficking
cell division
drug and TRH metabolizing enzyme
neutrophil-specific antigen
signal transduction and lipid biosynthesis
glycine cleavage system (mitochondrial)
unknown
blocks proteolytic activation of SREBPs by SCAP
circadian transcription factor
receptor for JAG1, JAG2 and Delta1 transcriptional activator, cell-fate
assembly/regulation of proteins in cornified envelope
lysine-degradation
export of lipids from ER to plasma membrane
apoptosis positive mediator induced by gamma-interferon
involved in p53-induced G2 cell cycle arrest
macrophage galactose-specific lectin
signaling
induced expression of ODC and AMD1 (polyamine biosynthesis).
formation of sphingosine 1-phosphate (SPP)
DNA repair
stress, hydroxyacylglutathione hydrolase, detoxifies methylglyoxal
catabolism of gamma-aminobutyric acid (GABA)
p53 induced chaperone for protein complexes in the respiratory chain
unknown
Ca(2+)-independent cell adhesion activity
formation of deoxyribonucleotides from corresponding ribonucleotides.
DNA binding, transferase activity
purine nucleoside transport
hepatic synthesis of glutathione
chemoattractant for dendritic cells and monocytes
steroid, vitamin D, and bile acid metabolism
mitochondrial
regulated destruction of mitotic cyclins A and B
cell surface protein
regulator of thrombospondin-1, Taxol sensitivity
glycolysis
covalent attachment of ubiquitin.
cyclin-dependent kinase related
glycolysis
PNRC1, FBXO11
Cldn1
Mal2
Sytl2
Ypel2
Pgpep1
Fcgr3
Agpat2
Gldc
EST
Insig2
BMAL1b, Arntl
NOTCH2
Scel
Aass
Oprs1
Dapk1
RPRM
MAC2
Ppp2r5a
Gfer, ALR
Sphk2
Xpc
Pnkd
ABAT
Cabc1
Cldn2
Rrm2
PAPD4
Slc28a2
Cth
HEBP1
Fdx1
Mrpl15
UBE2C
Pvrl2
Prr13
Pgk1
Psmd9
PFTK1
Pgk1
Supplementary Table 2: Cluster 2 Transcripts.
Probe
Set ID
1398282_at
1372056_at
1387203_at
1388348_at
1368778_at
1368036_at
1388642_at
1374531_at
1376709_at
1388566_at
1389169_at
1388531_at
1370374_at
1371519_at
1368426_at
1370928_at
1370975_at
1388422_at
1368294_at
1371969_at
1389156_at
1371251_at
1398994_at
1367718_at
1376572_a_at
1373015_at
1387183_at
1388659_at
1369902_at
1372844_at
1390172_at
1398273_at
1371632_at
1389965_at
1389681_at
1370345_at
1374939_at
1374765_at
1376038_at
1375775_at
1370940_at
1367537_at
1373864_at
1368769_at
1373722_at
1373730_at
1390697_at
Accession #
NM_053902
AI406687
NM_013120
BI278590
NM_017206
M60103
AI412114
AA926305
BM388442
AI102215
AA944158
BF283382
AF335281
AA851258
NM_031987
BI284739
AI172079
BI275904
NM_053907
BI291848
BM384589
L05541
BI301193
NM_017177
AI045848
BI280348
J02844
BI295783
NM_139258
AW531877
AI409946
NM_053599
AI231166
AA799818
BI296388
L11995
BE112927
BI288055
AI411054
BI296701
BG378746
AI012479
BM388810
NM_031760
BE111697
BI282077
BI278125
Correlation
0.98
0.967
0.959
0.952
0.947
0.946
0.931
0.929
0.921
0.92
0.917
0.916
0.904
0.899
0.897
0.895
0.887
0.879
0.879
0.878
0.876
0.875
0.873
0.87
0.861
0.858
0.856
0.854
0.853
0.853
0.852
0.85
0.85
0.849
0.843
0.832
0.83
0.829
0.822
0.814
0.801
0.8
0.796
0.786
0.773
0.767
0.763
Abbreviation
Gene Name
Gene Function
Kynu
Cmtm6
Gckr
ELOVL5
Slc6a6
Ptprf
EI24
Slc6a6
Slc39a8
Lasp1
Pgrmc2
Pgrmc2
STEAP3
Etfdh
Crot
Litaf, RFX4
JMJD1A
Lims2
Dnase1l3
CALD1
LOC498606
GALT
Tpst2
Chetk
SVIL
Rnf11
Crot
Carhsp1
Bmf
Efna1, B61
Dhtkd1
Efna1, B61
CORO1C
Tgoln2
Pvrl2
Ccnb1
Cyfip2
Bdh1
CDC42
ODF3
Tjp2
Eif4enif1
MAP3K4
Abcb11
Kif20a
RBM33
Gemin8
kynureninase (L-kynurenine hydrolase)
CKLF-like MARVEL transmembrane domain containing 6
Glucokinase regulatory protein
ELOVL family member 5, elongation of long chain fatty acids
solute carrier family 6 (taurine), member 6
protein tyrosine phosphatase, receptor type F
etoposide induced 2.4
solute carrier family 6 (taurine), member 6
solute carrier family 39 (metal ion transporter), member 8
LIM and SH3 protein 1
progesterone receptor membrane component 2
progesterone receptor membrane component 2
STEAP family member 3
electron-transferring-flavoprotein dehydrogenase
carnitine O-octanoyltransferase
regulatory factor X, 4 (influences HLA class II expression)
jumonji domain containing 1A
LIM and senescent cell antigen like domains 2
DNase gamma; deoxyribonuclease I-like 3
caldesmon 1
hypothetical protein LOC498606
galactose-1-phosphate uridyltransferase
protein-tyrosine sulfotransferase 2
choline kinase-like; choline/ethanolamine kinase
supervillin
ring finger protein 11
carnitine octanoyltransferase
calcium regulated heat stable protein 1
Bcl-2 modifying factor
ephrin A1
dehydrogenase E1 and transketolase domain containing 1
ephrin A1
Coronin, actin binding protein 1C
trans-Golgi network protein 2
poliovirus receptor-related 2
cyclin B
cytoplasmic FMR1 interacting protein 2
3-hydroxybutyrate dehydrogenase, type 1
cell division cycle 42 (GTP binding protein, 25kDa)
outer dense fiber of sperm tails 3
tight junction protein 2 (zona occludens 2)
eukaryotic translation initiation factor 4E nuclear import factor 1
mitogen-activated protein kinase kinase kinase kinase 4
ABC transport protein, sub-family B, member 11
kinesin family member 20A
RNA binding motif protein 33
gem (nuclear organelle) associated protein 8
tryptophan-nicotinic acid pathway, decreased formation of nicotinic acid
chemokine-like factor superfamily member 6
inhibits glucokinase
fatty acid elongase
taurine is involved in bile acid conjugation
signaling insulin
apoptosis, p53-induced genes
taurine is involved in bile acid conjugation
zinc transporter
regulation of dynamic actin-based, cytoskeletal activities
receptor
receptor
downstream of p53 to interface apoptosis and cell cycle progression
inner mitochondrial membrane
beta oxidation, transfer of fatty acyl groups between CoA and carnitine
winged-helix transcription factor
STAT3 signaling, transcription
adhesion sites between cells and the extracellular matrix
apoptosis
cytoskeletal remodeling
unknown
interconversion of galactose-1-phosphate and glucose-1-phosphate
posttranslational modification
first enzyme in phosphatidylcholine biosynthesis
link between actin cytoskeleton and membrane
modulator of growth factor receptor signalling and transcription
beta oxidation, transfer of fatty acyl groups between CoA and carnitine
IGF-I signaling, kinase substrate
proapoptotic members of the BCL2 family
receptor tyrosine kinase
oxoglutarate dehydrogenase (succinyl-transferring) activity
receptor tyrosine kinase
WD repeats
key sorting station for proteins, membrane traffic in secretory pathway
cell surface protein
complexes with p34 (cdc2) to form the mitosis-promoting factor
CYFIP2 is a direct p53 target responsible for p53-dependent apoptosis
mitochondrial membrane, specific requirement for phosphatidylcholine
delivery of newly synthesized proteins/lipids to plasma membrane
component of sperm flagella outer dense fibers
bile acid transport and circulation
translation
mediator of environmental stress, activates the CSBP2 MAPK pathway
major canalicular bile salt export pump
motor-driven transport processes that occur in mitotic cells
RNA binding
small nuclear ribonucleoprotein assembly
Supplementary Table 3: Cluster 3 Transcripts.
Probe
Set ID
1387156_at
1375941_at
1373986_at
1386946_at
1377921_at
1367836_at
1376868_at
1386987_at
1388901_at
1373777_at
1372715_at
1393516_at
1380905_at
1387228_at
1373625_at
1386960_at
1388872_at
1390530_at
1387038_at
1383013_at
1373282_at
Accession #
NM_024391
BI292120
AI410107
NM_031559
AA875050
U88294
BM389293
NM_017020
AW534837
BF391820
AA819349
AA892335
AA893260
NM_012879
AI412012
NM_031589
BI290053
AI169239
NM_053425
AI045857
AI406494
Correlation
0.987
0.975
0.968
0.96
0.956
0.943
0.94
0.939
0.938
0.929
0.909
0.9
0.887
0.881
0.871
0.868
0.868
0.852
0.85
0.807
0.804
Abbreviation
Gene Name
Gene Function
Hsd17b2
Baiap2l1
TNFSF11
Cpt1a
ETNK2
CPTI
Cobll1
Il6r
Fkbp5
RGS16
SLC25A1
Slc16a12
IL32
Slc2a2, Glut2
Shmt1
Slc37a4, G6pt1
Idi1
Slc16a12
Ccs
Klf13
SLC25A33
17-beta hydroxysteroid dehydrogenase type 2
BAI1-associated protein 2-like 1
tumor necrosis factor superfamily, member 11
carnitine palmitoyltransferase 1 alpha
ethanolamine kinase 2
carnitine palmitoyltransferase I
Cobl-like 1(Cordon-bleu)
interleukin 6 receptor .
FK506 binding protein 5
regulator of G-protein signaling 16
liver tricarboxylate carrier
solute carrier family 16, member 12
interleukin 32
solute carrier family 2 A2
serine hydroxymethyl transferase 1 (soluble)
solute carrier family 37 member 4
isopentenyl-diphosphate delta isomerase
solute carrier family 16 , member 12
copper chaperone for superoxide dismutase
Kruppel-like factor 13
mitochondrial carrier protein MGC4399
catalyzes interconversion of testosterone and androstenedione - as well as estradiol and estrone
cytoskeletal regulation and cellular organization
ligand for TNF receptor RANKL 'receptor activator of NF-kappa-B ligand'
fatty acid metabolism
first step of phosphatidylethanolamine (PtdEtn) biosynthesis
fatty acid metabolism
unknown
cell surface receptor linked signal transduction
glucocorticoid signaling, HSP90
inhibits G protein-coupled mitogenic signal transduction and activation (MAPK) cascade
mitochondria, solute carrier
monocarboxylic acid transporters: lactate, pyruvate
a cytokine and inducer of TNF alpha
low-affinity glucose transporter, type 2
folate metabolism biosynthesis of nucleotides and amino acids
transports glycerol-3-phosphate between cellular compartments
isoprenoid biosynthetic pathway
monocarboxylic acid transporters
copper chaperone
transcription F dominant transactivator of RANTES in T-cells
mitochondrial inner membrane
Supplementary Table 4: Cluster 4 Transcripts.
Probe
Set ID
1387109_at
1371580_at
1368213_at
1373842_at
1387852_at
1371012_at
1371400_at
1370150_a_at
1387848_at
1368275_at
1398819_at
1387703_a_at
1372602_at
1371498_at
1373668_at
1375549_at
1375852_at
1367982_at
1369270_at
1389430_at
1374709_at
1388874_at
1369467_a_at
1368460_at
1387244_at
1373870_at
1372533_at
1387805_at
1367771_at
1389256_at
1389480_at
1372085_at
1371363_at
1371524_at
1368878_at
1390448_at
1372141_at
1386927_at
1374251_at
1398240_at
1382255_at
1374903_at
1387780_at
1368365_at
1368852_at
1387856_at
1371031_at
1389738_at
1373383_at
1389301_at
1389717_at
1389639_at
1388136_at
1374820_at
1368068_a_at
1387017_at
1371843_at
1372642_at
1398832_at
1368458_at
1388102_at
1371147_at
1371463_at
1374288_at
Accession #
NM_031576
AI102725
AI407454
BM390718
NM_012703
AJ245707
AI169092
NM_012703
NM_013134
NM_080886
NM_022934
AF106659
BI295979
AI412685
BG373075
AI407719
BM390399
NM_024484
NM_052980
AI176172
AI406795
BE113032
NM_012621
NM_031741
NM_053899
BE110630
AI175790
NM_053420
NM_031345
BG381256
AI598462
AI237657
BI277042
AI009608
NM_053539
AA800699
BI289500
NM_012930
AA893192
NM_024351
BE110785
AI234819
NM_032079
NM_031731
BG668811
BI274457
AI454484
AA848420
AA848807
AI176665
AI171467
BF283302
BF282660
AI598946
NM_130740
NM_017136
AI234128
BE113397
NM_012749
NM_012942
U66322
X69834
AI233239
BG374267
Correlation
0.988
0.979
0.971
0.97
0.955
0.951
0.949
0.948
0.946
0.941
0.94
0.94
0.937
0.932
0.932
0.931
0.929
0.928
0.928
0.926
0.924
0.924
0.924
0.923
0.921
0.92
0.919
0.918
0.917
0.916
0.916
0.914
0.914
0.912
0.911
0.91
0.91
0.909
0.907
0.907
0.902
0.901
0.9
0.898
0.895
0.893
0.893
0.891
0.891
0.889
0.883
0.88
0.876
0.875
0.875
0.873
0.867
0.866
0.865
0.854
0.849
0.847
0.843
0.842
Abbreviation
Gene Name
Gene Function
Por
(Spfh1)
Por
(N-WASP)
Thrsp, Lpgp, SPOT1
Hpcl2
Thrsp, Lpgp, SPOT1
Thrsp, Lpgp, SPOT1
Hmgcr
Sc4mol
Hsj2, Dnaja1,Hsp40
ubp69, Usp2
SBP
JTV1, p38
Polr2i
Usp2
Hmgcr
Alas1
Nr1i2
Hsd17b7
HLF, PAR bZIP
Mtss1
Pfkfb1
Slc2a5
Cgr19
FAM98A
EDEM1
Bnip3
Gilz
NADPH-cytochrome P-450 oxidoreductase
SPFH domain family, member 1
P450 (cytochrome) oxidoreductase
neural Wiskott-Aldrich syndrome protein
thyroid hormone responsive protein
2-hydroxyphytanoyl-CoA lyase.
thyroid hormone responsive protein
thyroid hormone responsive protein
3-hydroxy-3-methylglutaryl-Coenzyme A reductase
sterol-C4-methyl oxidase-like
DNAJ (Hsp40) homolog, subfamily A, member 1
ubiquitin-specific, cysteine protease
genethonin 1
tRNA synthetase cofactor p38
polymerase (RNA) II polypeptide I
ubiquitin specific peptidase 2
3-hydroxy-3-methylglutaryl-Coenzyme A reductase
aminolevulinic acid synthase 1
nuclear receptor subfamily 1, group I, member 2
hydroxysteroid (17-beta) dehydrogenase 7
hepatic leukemia factor
metastasis suppressor 1
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1
solute carrier family 2, member 5
cell growth regulatory with ring finger domain
family with sequence similarity 98, member A
ER degradation enhancer, mannosidase alpha-like 1
BCL2/adenovirus E1B 19 kDa-interacting protein 3
glucocorticoid-induced leucine zipper
EST
RWD domain containing 4A
DP-ribosylation factor-like 6 interacting protein 2
glycerol-3-phosphate dehydrogenase 1 (soluble)
trap locus 3 , transcription factor IIB-like
isopentenyl-diphosphate delta isomerase
abhydrolase domain containing 13
prefoldin subunit 2
carnitine palmitoyltransferase 2 (Cpt2)
potassium inwardly-rectifying channel, subfamily J, member 15
heat shock cognate protein 70; heat shock 70kD protein 8
visfatin, pre-B-cell colony-enhancing factor 1
beta-1,6-acetylglucosaminyltransferase family polypeptide 3
DNAJ (Hsp40) homolog, subfamily A, member 2
alcohol/aldehyde dehydrogenase family 3, subfamily A2
DNAJ-like 2 heat-shock 40-kd protein 4
calponin 3, acidic
methionine adenosyltransferase I, alpha
uracil-DNA glycosylase
MTERF domain containing 1
muscle blind-like 2 isoform 1
KIAA0157
protocadherin 1 (cadherin-like 1)
translocase of inner mitochondrial membrane 9
l(3)mbt-like 4 (Drosophila)
protein kinase C and casein kinase substrate 2
squalene epoxidase
Yip1 domain family, member 5
E1 small nucleolar RNA gene
nucleolin
cytochrome P450 (cholesterol hydroxylase 7 alpha)
dithiolethione-inducible gene-1
serine protease inhibitor 2.4
PHD finger protein 5A
FtsJ homolog 3 (E. coli)
donates electrons to all microsomal P450 enzymes
ER lipid raft associated 1
donates electrons to all microsomal P450 enzymes
transmission of signals from tyrosine kinase receptors and small GTPases to cytoskeleton
activates genes encoding the enzymes of fatty acid synthesis
peroxisome, alpha-oxidation of 3-methyl-branched fatty acids
activates genes encoding the enzymes of fatty acid synthesis
activates genes encoding the enzymes of fatty acid synthesis
rate-limiting step in cholesterol biosynthesis
cholesterol biosynthesis
partners for Hsp70 chaperones
disassembly of polyubiquitin chains
starch binding protein
transcription of genes encoding mRNA
DNA directed
disassembly of polyubiquitin chains
rate-limiting step in cholesterol biosynthesis
rate-limiting enzyme in heme biosynthesis (mitochondrial)
pregnane X receptor (PXR) activates cytochrome P450-3A, xenobiotic and drug metabolism
oxidizes or reduces estrogens and androgens
proline and acidic amino acid-rich basic leucine zipper transcription factor family (circadian)
regulator of cytoskeletal dynamics, interacts with ATP-actin monomers
glycolysis
facilitated glucose transporter
p53 related, inhibits growth
unknown
accelerates degradation of misfolded proteins in ER
pro-apoptotic mitochondrial protein
glucocorticoid-induced leucine zipper, inhibits NF-B activity
unknown
ubiquitin protein ligase activity
translocation of proteins across ER membrane
triglyceride synthesis
transcription initiation in eukaryotes is mediated by the TATA-binding protein
peroxisomal, isoprenoid biosynthetic pathway
triglyceride storage
molecular chaperone, assists in correct folding of other proteins
fatty acid metabolism
bile, maintains charge balance during bile secretion
molecular chaperone, assists in correct folding of other proteins
type II phosphoribosyltransferase enzyme involved in NAD biosynthesis
Golgi, glycoprotein synthesis
partners for Hsp70 chaperones
catalyzes oxidation of long-chain aldehydes derived from lipid metabolism
partners for Hsp70 chaperones
cytoskeleton
catalyzes formation of adenosylmethionine from methionine and ATP
DNA repair enzyme
mitochondrial transcription termination factor
triplet-expansion RNA-binding protein
unknown
mediates calcium-dependent cell-cell adhesion.
import and insertion of hydrophobic proteins into mitochondrial inner membrane
changes in chromatin organization, cell cycle
organization of actin cytoskeleton and regulation of vesicular traffic
cholesterol biosynthesis catalyzes the first oxygenation step in sterol biosynthesis
intracellular trafficking (Golgi) , Rab GTPases
interacts directly with unique segments of pre-rRNA
transcription of ribosomal RNA genes by RNA polymerase I, ribosome maturation
catalyzes first step in bile acid synthesis
inhibits pro-inflammatory actions of LTB4
plasma protein
pre-mRNA splicing, transcriptional regulator
ribosome assembly, rRNA methyltransferase 3
Rwdd4a
Arl6ip2
Gpd1
(Gtl3)
Idi1
Abhd13
PFDN2
Cpt2
Kir4.2, KCNJ15
Hspa8
PBEF1
Ignt3
Dnaja2
Aldh3a2
Hsj2
Cnn3
Mat1a
Ung
Mterfd1
MBNL1
PCDH1
Timm9
L3MBTL4
Pacsin2
Sqle
Yipf5
RNU17A
Ncl
Cyp7a1
DIG-1
SERPINA3
phf5a
FTSJ3
Supplementary Table 4: Cluster 4 Transcripts Cont’d.
Probe
Set ID
1377042_at
1387233_at
1371596_at
1371543_at
1372320_at
1367541_at
1375280_at
1370663_at
1372115_at
1389561_at
Accession #
BI288196
NM_017235
AI008971
AI170047
BE103894
BE113965
AW913871
D31838
AI408477
BE110624
Correlation
0.827
0.826
0.821
0.81
0.81
0.809
0.807
0.804
0.803
0.781
Abbreviation
Gene Name
Gene Function
PCGF5,
Hsd17b7
Rnps1
Mtmr2
Msl31
METTL5
PNAS-4
wee1
UBR2
polycomb group ring finger 5
hydroxysteroid (17-beta) dehydrogenase 7
ribonucleic acid binding protein S1
myotubularin related protein 2
male-specific lethal-3 homolog 1
methyltransferase like 5
apoptosis-related protein PNAS-4
wee1 tyrosine kinase
ubiquitin protein ligase E3 component n-recognin 2
EST
chromatin remodeling
oxidizes or reduces estrogens and androgens
regulates alternative splicing of variety of pre-mRNAs
protein-tyrosine phosphatase, non-receptor
chromatin remodeling and transcriptional regulation
DNA methylation
protein targeting
phosphorylates p34(CDC2), coordinates transition between DNA replication and mitosis
recognize substrate's destabilization signal, proteolysis
unknown
Supplementary Table 5: Cluster 5 Transcripts.
Probe
Set ID
1371693_at
1371418_at
1388898_at
1399058_at
1372701_at
1387336_at
1371976_at
1375336_at
1371763_at
1399082_at
1371770_at
1398315_at
1371505_at
1383160_at
1388629_at
1371634_at
1371403_at
1389412_at
1372752_at
1375335_at
1370163_at
1398877_at
1387659_at
1369976_at
1388325_at
1398937_at
1371916_at
1388528_at
1373319_at
1373913_at
1370299_at
1388424_at
1371957_at
1367670_at
1371372_at
1398317_at
1382048_at
1398885_at
1387062_a_at
1398871_at
1367606_at
1388534_at
1373472_at
1389384_at
1398761_at
1388108_at
1370062_at
1389658_at
1371435_at
1368049_at
1376252_at
1387793_at
1372688_at
1398749_at
1371445_at
1392928_at
1367686_at
1388117_at
1371564_at
1368328_at
1372318_at
1367983_at
1398349_at
1368230_a_at
Accession #
AA849757
BG665035
AI236601
BI288800
AI237597
NM_022635
AI102758
AI237389
BI274533
AI176581
AW434268
AA800007
BG381750
AA892238
BF281278
BE107851
AA799545
AA800693
BF282632
BI285700
BF281299
BI283691
AF245172
NM_053319
BF281358
BI279381
AI409380
AW433875
BF419628
BF282271
M10149
AI407015
BM388851
NM_017005
AA944161
BF283428
BI289589
AA925327
NM_080400
BG671311
NM_017153
AA851369
AI177008
BE111733
NM_031099
BE116152
NM_080902
BI283104
BI279561
NM_012670
AI145784
NM_021594
BI296190
NM_022510
BF285649
AA891693
NM_030835
AI411893
AI169159
NM_013089
AI235528
NM_053430
AI411497
U95161
Correlation
0.984
0.98
0.977
0.972
0.97
0.969
0.968
0.965
0.964
0.959
0.956
0.949
0.945
0.943
0.943
0.942
0.942
0.941
0.94
0.939
0.939
0.936
0.934
0.934
0.933
0.929
0.929
0.926
0.925
0.921
0.92
0.919
0.918
0.914
0.909
0.905
0.902
0.899
0.897
0.896
0.894
0.893
0.892
0.891
0.891
0.889
0.888
0.888
0.886
0.885
0.884
0.881
0.88
0.88
0.878
0.878
0.874
0.87
0.866
0.865
0.862
0.855
0.855
0.854
Abbreviation
Gene Name
Gene Function
AHSA1
CCT2
Hsph1
Mrpl18
Hsp1a
Cml4
EST
hsp84
EST
Tmem33
Ke2
Rpl15
Hnrpc
Chordc1
Impdh2
TMEM126A
Cct3
ZNF306
Tspan4
Hsp90
Odc1
Stip1
Gda
Pin
Atp6v1d
Dhx15
SEPX1
Fbl
Ddx1
Pnpt1
Aldob
Eif3s1
IMP4
Fh1
p23
Bpnt1
MYO1D
Rpl23
Chek1
Rpl17
Rpls3a
SLC31A1
Actr6
Hrpap20
Rpl5
ELO2
Hig1
Nsun2
Naca
Tcp1
SRp20, Sfrs3
Slc9a3r1
Exosc7
Rpl4
p34
PXMP3
RAMP4, SERP1
Snrpb
Atp6v1e1
Gys2
ELOVL6
Fen1
Ak2
LOC56769
activator of heat shock 90 kDa protein ATPase homolog 1
chaperonin containing TCP1, subunit 2 (beta)
heat shock 105 kDa/110k Da protein 1
mitochondrial ribosomal protein L18
heat shock protein 1, alpha
N-acetyltransferase Camello 4
EST
heat shock protein 84
EST
transmembrane protein 33
MHC class II region expressed gene KE2
ribosomal protein L15
heterogeneous nuclear ribonucleoprotein C
cysteine and histidine-rich domain (CHORD)-containing, zinc-bp1
inosine 5-monophosphate dehydrogenase 2
transmembrane protein 126A
chaperonin subunit 3 (gamma)
zinc finger protein 306
tetraspanin 4
heat shock 90 kDa protein 1, beta
ornithine decarboxylase 1
stress-induced phosphoprotein 1
guanine deaminase
dynein, cytoplasmic, light chain 1
ATPase, H+ transporting, V1 subunit D
DEAH (Asp-Glu-Ala-His) box polypeptide 15
selenoprotein X, 1
fibrillarin
DEAD (Asp-Glu-Ala-Asp) box polypeptide 1
polyribonucleotide nucleotidyltransferase 1
aldolase B
eukaryotic translation initiation factor 3, subunit 1 alpha
IMP4, U3 small nucleolar ribonucleoprotein
fumarate hydratase
stimulated the intrinsic ATPase activity of HSP90
cyclin E accumulation, partner of cyclin-dependent kinase 2, positive control of the G1/S transition
chaperone activity
mitochondrial
chaperone activity
drug metabolism in the liver
unknown
chaperone activity
unknown
multipass membrane protein
centromeric end of major histocompatibility complex
60S ribosomal subunit structure
major constituents of ribonucleoprotein particles
binds to HSP90
de novo synthesis of guanine nucleotides, regulation of cell growth
mitochondrial
chaperone, VHL protein (tumor suppressor)
transcriptional regulation
complexes with integrins and other cell-surface proteins
chaperone activity
cell cycle, biosynthesis of polyamines
association of molecular chaperones HSP70 and HSP90
catalyzes the hydrolytic deamination of guanine
effects nitric oxide synthase activity
vacuolar-type proton pump, ATPase transport
ATP-dependent RNA helicase, pre-mRNA splicing factor
scavenging of ROS, oxidative stress
component of nucleolar small nuclear ribonucleoprotein particle, processing preribosomal RNA
RNA helicase translation initiation, splicing, and ribosome and splicesome assembly
exosome complex, RNA processing and degradation
glycolysis
translation
ribosomal protein
krebs cycle, fumarate to malate (mitochondrial)
HSP-90 chaperone p23, coupled to prostaglandin-endoperoxide H synthase-1
nucleotide metabolism
molecular motors, intracellular movements
60S ribosomal subunit
timing of cell cycle transitions, DNA damage checkpoint
60S ribosomal subunit
ribosome biogenesis; protein biosynthesis
high-affinity copper uptake
role in heterochromatin formation (nuclear)
phosphoprotein that is required for proliferation and survival of hormone-dependent tumor cells
chaperone for the 5S rRNA
fatty acid synthesis
protects cells from apoptosis
methyltransferase, disassembly of the nucleolus during mitosis, methylates RNA polymerase III
chaperone/stress, prevents inappropriate targeting of non-secretory polypeptides
cytosolic chaperone, folding of newly translated proteins in cytosol
SR family of mRNA splicing factors, consecutive serine (S) and arginine (R) dipeptides
actin cytoskeleton reorganization requires activation of a sodium/hydrogen exchanger
rapid degradation of ARE-containing RNAs
60S ribosomal subunit
ribosome binding
peroxisome assembly
stabilization of membrane proteins in response to stress
pre-mRNA splicing
vacuolar-type proton pump ATPase transport
glucose storage
fatty acid synthesis
removes 5-prime overhanging flaps in DNA repair and synthesis
mitochondrial enzyme, ATP:AMP phosphotransferase
unknown function
prostaglandin E synthase 3, telomerase-binding p23, Hsp90 co-chaperone
bisphosphate 3'-nucleotidase 1
myosin ID
ribosomal protein L23
checkpoint kinase 1
ribosomal protein L17
ribosomal protein S3a
solute carrier family 31, member 1
ARP6 actin-related protein 6 homolog (Actr6)
hormone-regulated proliferation associated protein 20
ribosomal protein L5
fatty acid elongase 2
HIG1 domain family, member 1A, hypoxia-inducible gene 1
NOL1/NOP2/Sun domain family, member 2
nascent-polypeptide-associated complex alpha polypeptide
T-complex 1
splicing factor, arginine/serine-rich 3 (SRp20)(Sfrs3)
solute carrier family 9 (sodium/hydrogen exchanger) isoform 3 regulator 1
exosome component 7
ribosomal protein L4
leucine-rich-repeat-protein superfamily; p34 protein, ribosome binding
peroxisomal membrane protein 3, 35kDa (Zellweger syndrome)
ribosome associated membrane protein 4
small nuclear ribonucleoprotein polypeptides B and B1
ATPase, H+ transporting, V1 subunit E isoform 1
glycogen synthase 2
ELOVL family member 6, elongation of long chain fatty acids
flap structure-specific endonuclease 1
adenylate kinase 2
nuclear protein E3-3
Supplementary Table 5: Cluster 5 Transcripts Cont’d.
Probe
Set ID
1389344_at
1371873_at
1376849_at
1375181_at
1368303_at
1389420_at
1373162_at
1372489_at
1388331_at
1373277_at
1398896_at
1369560_at
1380547_at
1370305_at
1367480_at
1369962_at
Accession #
BE109258
AA850735
BM384872
AI170643
NM_031678
BI279446
AI600085
AI172498
BG057543
BG373457
AA892567
NM_022215
BI288519
U96490
AI230248
NM_031014
Correlation
0.854
0.851
0.85
0.848
0.838
0.838
0.835
0.832
0.831
0.827
0.807
0.802
0.801
0.793
0.77
0.759
Abbreviation
Gene Name
Gene Function
Usp39
ANP32E, Cpd1
Usp48
Rpl12
Per2
Stap2
Tmem41a
Slap
Hsp90B1
Tm2d3
Arcn1
Gpd3
CLCN3
Yif1p
Dhx15, EIF4A3
Atic
ubiquitin specific protease 39
acidic (leucine-rich) nuclear phosphoprotein 32 family, member E
ubiquitin specific protease 48
ribosomal protein L12
period homolog 2 (Drosophila)
signal-transducing adaptor protein-2
transmembrane protein 41a
sarcolemma associated protein
heat shock protein 90 kDa beta (Grp94), member 1(HSP90B1)
TM2 domain containing 3
archain 1
glycerol 3-phosphate dehydrogenase
chloride channel 3
Yip1 interacting factor homolog A
DEAD (Asp-Glu-Ala-Asp) box polypeptide 48
possible competitor of ubiquitin C-terminal hydrolases (UCHs)
nucleo-cytoplasmic shutteling phosphoprotein, chromatin remodeling, transcription regulation
protein ubiquitination
60S ribosomal subunit
regulation of transcription
signal-transducing adaptor molecule, links several tyrosine kinases and STAT3
multipass membrane protein
chaperone activity
chaperone activity
G protein-coupled receptor
coatomer associates with Golgi, biosynthetic protein transport from the ER
lipid and carbohydrate metabolism
voltage-gated chloride channel
interacts with Yip1
eukaryotic translation initiation actor 4A, isoform 3
de novo purine biosynthesis
5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase